Small cell carcinoma of the rectum (SCCR) is a rare and aggressive neuroendocrine tumor. Its association with a tubulovillous adenoma is an exceptional occurrence, presenting significant implications for diagnosis and treatment. This case report details a 62-year-old male, undergoing treatment for hepatocellular carcinoma, presented with symptoms of diarrhea. A colonoscopy initially suggested a benign tubulovillous adenoma, but the presence of discordant clinical findings led to further evaluation. The final diagnosis, established post-surgery, was SCCR originating from a tubulovillous adenoma. This case highlights the diagnostic challenges when unusual presentations arise from atypical pathological findings, especially in patients with concurrent malignancies. The management followed standard care protocols, including robotic transanal surgery, despite the patient's ongoing HCC treatment. This case adds to the limited existing literature on SCCR, particularly its rare association with a tubulovillous adenoma. It emphasizes the importance of a multi-disciplinary approach in diagnosing and managing rare entities in colorectal cancer while demonstrating the feasibility of standard care in patients with complex comorbidities.